Peter Kerr NCRI Informatics Unit

Using informatics to maximise the impact of cancer research

The NCRI Partnership

What is the role of the NCRI?

• Strategic oversight of cancer research in the UK• Identify gaps and opportunities• Plan and co-ordinate approaches between funding

bodies• Monitor progress• A ‘Virtual Institute’ co-funded by Government &

Charities

• Focus of activity• Co-ordination and strategic planning• National Infrastructure issues

The NCRI Cancer Informatics Initiative

• NCRI Board identified cancer informatics as an area of focus

In this context informatics is defined as the research, development, or application of computational tools and approaches for expanding the use of biological, medical, or health data, including those to acquire, store, organise, archive, analyse, or visualise such data.

History

• National Advisory Panel for Bioinformatics met and developed ‘NCRI Strategic Framework for the Development of Cancer Research Informatics’

• Strategic Framework approved by NCRI Board

• Funding from CRUK, MRC, DH, ICR, AstraZeneca

• NCRI Informatics Unit established

• Statement of Intent published in Nature and the BMJ

Management Structure

NCRI Board

HLSC

Task Force Unit

Chair of Informatics Task Force

Data Sharing Committee

Prof Alex Markham (Chair, Chief Executive, Cancer Research UK)

Prof Sally Davies (Director of Research, Department of Health)

Prof Mike Richards (National Cancer Director)

Prof John Williams (Director Health Informatics, Royal Coll Phys)

Prof Colin Blakemore (Chief Executive, MRC)

Prof Mark Walport (Director, Wellcome Trust)

Dr Philip Campbell (Editor-in-Chief, Nature)

Prof Tony Hey (Director, e-Science Core Programme)

Mrs Joanne Rule (Chief Executive, Cancer BACUP)

Professor Alan Horwich (Caldicott Guardian)

Dr Ken Buetow (NCI)

Industry Representative (TBA)

NCRI Cancer Informatics High-Level Implementation Steering Committee

NCRI Informatics & Strategic Partnerships

NCRI Informatics

Unit

NCTR

‘omics’ – High-throughput techniques

30,000 genes

100,000 – 200,000proteins

‘omics’ – High-throughput techniques

30,000 genes

100,000 – 200,000proteins

Van de Vijver et al, 2002

Tumour response to chemotherapy

Data issues

• Large amount of data

• Lack of data standards

• Lack of interoperability between databases

NCRI Strategic Framework for the Development of Cancer Research Informatics

2 key points:

Common data standards should be adopted

Data sharing should be the norm

Progress

• Development of Framework and initial implementation

• Mapping projects, standards and resources on to a matrix

• Development of a data sharing policy with the funders

• Communicating with the community through website, presentations

Draft NCRI Data Sharing Policy

The NCRI member organisations agree the following:

- Publicly funded research data should be openly available to the maximum extent possible unless appropriate consent or ethical approval have not been gained, the confidentiality of study participants can not be safeguarded, or there are IP issues that are of concern to a potential or existing commercial partner

- In the long-term, all cancer-related research applications should include a data sharing strategy and NCRI Partners will implement this in a step-wise fashion over coming academic sessions

- Data should be shared in a timely and responsible fashion

- NCRI Partner Organisations recognise that there may be a cost to allow data management that enables sharing

- NCRI Partner Organisations will provide applicants with advice on how to develop a data sharing strategy and recommend that applicants use data use agreements to govern the use of their data

- NCRI Partner Organisations will assess the validity of data sharing strategies and monitor their progress as part of their normal review mechanisms

SCIENCE & TECHNOLOGY

Clinical trials

The sounds of silenceSep 9th 2004 From The Economist print edition

Negative clinical-trial results are underreported. But this may soon change

SOMETIMES, no news is news. In clinical trials, where new medical treatments are tried out on human subjects, no news—an inconclusive result, indicating that the treatment is useless, or a negative one, indicating that it is harmful—can be as scientifically important as a positive result. Unfortunately, such a result is much less likely to be reported.

That is particularly true for trials sponsored by the pharmaceutical industry which, according to the American Medical Association (AMA), accounted for over 70% of the funding for such trials in America in 2002, the most recent year for which figures are available. The lack of reporting of null or negative findings is pernicious because it skews the results of so-called “meta-analyses”, which compile data from previous studies of a treatment. If only positive results are reported, then a meta-analysis risks being too laudatory.

The medical profession has been aware of this problem for a long time. However, pharmaceutical companies have a vested interest in keeping negative results quiet, so change has been slow in coming. But the proper balance between commercial confidentiality and public disclosure in the case of drugs, where ignorance can cost lives through misprescription, is different from that for, say, computer chips. The widespread government funding of basic drug research also gives the public a moral claim on the results. And a confluence of forces in the past few weeks may well succeed in pushing drug companies towards greater openness.

Informatics Website

• www.cancerinformatics.org.uk

• Information resource for the Funders, scientific and clinical communities and the Unit

• Main point of contact with relevant communities

• The matrix is a unique information resource

• Constantly being updated

Areas of Focus

• Conceptual Modelling

• Imaging and Pathology

• Clinical Trials and Functional Genomics

• Human Genetic Variation

Platform Reference ModelApproach

The first steps in achieving this aim:• understand what the key components of such a platform

are for different user groups within the cancer research domain

• to understand what goals this platform is required to serve for the community and to determine the feasibility and resources needed

• to understand what resources are available that can contribute to the construction of the platform

• consider interoperability requirements and how that might be acheived

Scientist

Microarray Data retrieval

ArrayExpress web services

ArrayExpress

MAGE-OM

MAGE-ML

Cancer patient

BioMoby

Tissue acquisition

Ethical approval via COREC

MyGrid Services Ontology

MGED ontology

Sample Info

Experimenter

Data release /access agreement

Functional Genomics and Clinical Trials

• Functional genomics community relatively mature in terms of data sharing

• Clinical trials increasingly incorporating high-throughput data

• Examining links between genomics, proteomics and clinical trials disciplines

electronic Remote Data Capture (e-RDC) Project

• Phase I pilot completed December 2003

- proved e-RDC useful for the collection and storage of real patient information in a clinical trial

• Phase II will be a multi-centre, multi-trial study to demonstrate scalability and explore the full functionality of a clinical data management system with e-RDC

National Cancer Research Network

• Established to provide the National Health Service (NHS) with an infrastructure to support prospective clinical trials of cancer treatments and other well-designed studies and to integrate and support research undertaken by cancer charities.

• Its aim is to improve the speed, quality and integration of research, ultimately resulting in improved patient care.

• The NCRN is increasing involvement and recruitment into clinical trials via the creation of 34 cancer research networks across England, closely aligned to cancer service networks.

• NCRN funding is allocated to networks to appoint research staff, such as research nurses, data managers and medical staff sessions and to access pharmacy, pathology, radiology and other areas of support, such as information systems and training, all of which are integral to high quality research.

National TRAnslational Cancer Research Network

• A national network of 14 cancer research centres, embedded in the NHS, that integrates scientific and clinical expertise, and shares knowledge and resources for the benefit of cancer patients.

• Initiatives in: BiotherapeuticsEthicsGenetics and Genomics DataNCTRWorking with IndustryQuality AssuranceTuBafrost

National Cancer Tissue ResourceBiology and Treatment Development  

• Unified national approach to the large-scale collection of high quality biological samples linked to clinical outcome data was needed.

• NTRAC led work on behalf of the NCRI funders to develop proposals for a National Cancer Tissue Resource (NCTR) – blueprint produced in 2002

• It is recommended that the NCTR comprises a managed network of tissue acquisition and processing centres, embedded within the NHS, underpinned by a state-of-the-art bioinformatics hub.

• Significant joint funding for the NCTR was announced in 2003 by the Department of Health (DH), the Medical Research Council (MRC) and Cancer Research UK (CRUK).

NCRI asked NTRAC to take forward 3 key strands of work to underpin the establishment of the NCTR:

- NCTR is implemented according to highest ethical standards;

- develop high-level operational framework;

- design and development of the information system underpinning the NCTR, including NCTR Centre specification

• The NCTR will facilitate research that advances cancer therapeutics and diagnostics from the laboratory to the clinic and will ultimately provide benefit for UK citizens. This initiative is an important development for cancer research and depends upon the willingness of surgical patients to engage with researchers to combat cancer by donating surplus surgical samples to the national resource.

NCTR Overview

NCRI NCTR Information System Outline Process Architecture